No, TX copied the entire Homebrew Launcher and large portions of Atmosphere and made small alterations to them in order to pass .XCI backups to the OS and bypass signature verification. Atmosphere doesn't have a specific mechanism for launching backups, that's correct, but that doesn't mean the fundamental components for it aren't implemented. This isn't a Ship of Theseus situation, it's more analogous to taking a Raspberry Pi and calling it a computer you built all by yourself.
Did you know that TX charging only for back up loader feature ? You can use SX OS for home-brew freely like atmosphere does, so even thought they used it but still they are not charging. They have created a new feature that does not exist in Atmosphere and asked us to pay for it in order to implement and also to get support (paying money for premium service) for OS in future updates, so its not just one time development and already they released 2 updates. Well you could say they might have used some research and few bits from that (mostly these days everyone make use of others research in some way to build rather reinventing the wheel, thats how the world works today), but does not mean its just complete copy.
They are charging for back up loader, and if its easy to replicate then already we should have open source back up loader by now based on atmosphere research which could have hunted TX more than making people to be worried about using SX OS. It would have been better if atmosphere developers shared detailed write up first to prove what they are talking rather just some random bits every few days.
TX is shady we know, and only way to hurt them right now is to make a free open source back loader or just release detailed analysis of SX OS like how it might affect users in regular usage. Even the people who are saying have reputation doing good work for community before but they will not get free passes to believe whatever they say unless proven. Right now TX has kept what they promised with SX OS for the people who paid, and have not got any bricks. Lets see what the write up from atmosphere developers have, and then decide who is right.